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- __builtin__.object
-
- euclidean_match_symmetry
- match_refine
- model_matches
- position
- cctbx.crystal.special_position_settings(cctbx.crystal.symmetry)
-
- model
class match_refine(__builtin__.object) |
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Methods defined here:
- __init__(self, tolerance, ref_model1, ref_model2, match_symmetry, add_pair_ext, i_pivot1, i_pivot2, eucl_symop, initial_shift, times=None)
- add_pairs(self)
- apply_eucl_ops(self, i_model2)
- calculate_rms(self)
- calculate_shortest_diff(self, pair)
- calculate_shortest_diffs(self)
- calculate_shortest_dist(self, pair)
- eliminate_weak_pairs(self)
- exclude_pairs(self)
- refine_adjusted_shift(self)
- show(self, f=None, truncate_singles=None, singles_per_line=5)
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class model(cctbx.crystal.special_position_settings) |
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- Method resolution order:
- model
- cctbx.crystal.special_position_settings
- cctbx.crystal.symmetry
- __builtin__.object
Methods defined here:
- __getitem__(self, key)
- __init__(self, special_position_settings, positions=None)
- __len__(self)
- add_position(self, pos)
- add_positions(self, positions)
- as_xray_structure(self, scatterer=None)
- cb_op(self)
- change_basis(self, cb_op)
- change_hand(self)
- expand_to_p1(self)
- positions(self)
- reset_cb_op(self)
- show(self, title, f=None)
- size(self)
- transform_to_reference_setting(self)
Methods inherited from cctbx.crystal.special_position_settings:
- assert_min_distance_sym_equiv(self)
- asu_mappings(self, buffer_thickness, sites_frac=None, sites_cart=None, site_symmetry_table=None, asu_is_inside_epsilon=None)
- incremental_pairs(self, distance_cutoff, asu_is_inside_epsilon=None, asu_mappings_buffer_thickness=-1, cubicle_epsilon=-1)
- min_distance_sym_equiv(self)
- pair_asu_table(self, distance_cutoff, sites_frac=None, sites_cart=None, site_symmetry_table=None, asu_mappings_buffer_thickness=None, asu_is_inside_epsilon=None, distance_cutoff_epsilon=None)
- site_cluster_analysis(self, min_distance=None, min_cross_distance=None, min_self_distance=None, general_positions_only=False, estimated_reduction_factor=4, asu_is_inside_epsilon=None, asu_mappings_buffer_thickness=-1, cubicle_epsilon=-1)
- site_symmetry(self, site)
- site_symmetry_table(self, sites_frac=None, sites_cart=None)
- sym_equiv_sites(self, site)
- u_star_tolerance(self)
Methods inherited from cctbx.crystal.symmetry:
- as_reference_setting(self)
- average_b_cart(self, b_cart)
- average_u_cart(self, u_cart)
- best_cell(self, angular_tolerance=None)
- build_miller_set(self, anomalous_flag, d_min, d_max=None)
- cell_equivalent_p1(self)
- change_of_basis_op_to_best_cell(self, angular_tolerance=None, best_monoclinic_beta=True)
- change_of_basis_op_to_inverse_hand(self)
- change_of_basis_op_to_minimum_cell(self)
- change_of_basis_op_to_niggli_cell(self, relative_epsilon=None, iteration_limit=None)
- change_of_basis_op_to_primitive_setting(self)
- change_of_basis_op_to_reference_setting(self)
- customized_copy(self, unit_cell=<class libtbx.utils.Keep at 0x9ce410>, space_group_info=<class libtbx.utils.Keep at 0x9ce410>)
- direct_space_asu(self)
- gridding(self, d_min=None, resolution_factor=None, step=None, symmetry_flags=None, mandatory_factors=None, max_prime=5, assert_shannon_sampling=True)
- inverse_hand(self)
- is_compatible_unit_cell(self)
- is_patterson_symmetry(self)
- is_similar_symmetry(self, other, relative_length_tolerance=0.01, absolute_angle_tolerance=1.0)
- join_symmetry(self, other_symmetry, force=False)
- minimum_cell(self)
- niggli_cell(self, relative_epsilon=None, iteration_limit=None)
- patterson_symmetry(self)
- primitive_setting(self)
- reflection_intensity_symmetry(self, anomalous_flag)
- show_summary(self, f=None, prefix='')
- space_group(self)
- space_group_info(self)
- special_position_settings(self, min_distance_sym_equiv=0.5, u_star_tolerance=0, assert_min_distance_sym_equiv=True)
- subtract_continuous_allowed_origin_shifts(self, translation_cart)
- unit_cell(self)
Data descriptors inherited from cctbx.crystal.symmetry:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class model_matches(__builtin__.object) |
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Methods defined here:
- __init__(self, model1, model2, tolerance=1.0, models_are_diffraction_index_equivalent=False, break_if_match_with_no_singles=False, rms_penalty_per_site=0.050000000000000003)
- consensus_model(self, i_model=1, i_refined_matches=0)
- n_matches(self)
- n_pairs_best_match(self)
- transform_model(self, i_model, i_refined_matches=0)
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class position(__builtin__.object) |
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Methods defined here:
- __init__(self, label, site)
- __repr__(self)
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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